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Fixed README

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Anthony Scemama 2021-11-01 10:23:47 +01:00
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README.md
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@ -20,7 +20,7 @@ TREX library for efficient I/O.
1. Download the `trexio-<version>.tar.gz` file 1. Download the `trexio-<version>.tar.gz` file
2. `gzip -cd trexio-<version>.tar.gz | tar xvf -` 2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
3. `cd trexio-<version>` 3. `cd trexio-<version>`
4. `./configure --enable-silent-rules` 4. `./configure`
5. `make` 5. `make`
6. `make check` 6. `make check`
7. `sudo make install` 7. `sudo make install`
@ -40,7 +40,7 @@ TREX library for efficient I/O.
1. `git clone https://github.com/TREX-CoE/trexio.git` 1. `git clone https://github.com/TREX-CoE/trexio.git`
2. `cd trexio` 2. `cd trexio`
3. `./autogen.sh` 3. `./autogen.sh`
4. `./configure --enable-maintainer-mode` 4. `./configure`
5. `make` 5. `make`
6. `make check` 6. `make check`
7. `sudo make install` 7. `sudo make install`
@ -54,7 +54,7 @@ Once installed, add `-ltrexio` to the list of compiler options.
In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`. In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
In order to link the program against TREXIO, the search paths can be modified as follows: In order to link the program against TREXIO, the search paths can be modified as follows:
`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib` `export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
(same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation. (same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation.
@ -78,28 +78,28 @@ The primary TREXIO API is composed of the following functions:
- `trexio_has_[group]_[variable]` - `trexio_has_[group]_[variable]`
- `trexio_close` - `trexio_close`
where `[group]` and `[variable]` substitutions correspond to the contents of the `trex.json` configuration file where `[group]` and `[variable]` substitutions correspond to the contents of the `trex.json` configuration file
(for more details, see the corresponding [documentation](https://trex-coe.github.io/trexio/trex.html) page). (for more details, see the corresponding [documentation](https://trex-coe.github.io/trexio/trex.html) page).
For example, consider the `coord` variable (array), which belongs to the `nucleus` group. The TREXIO user can write or read it using `trexio_write_nucleus_coord` or `trexio_read_nucleus_coord` functions, respectively. For example, consider the `coord` variable (array), which belongs to the `nucleus` group. The TREXIO user can write or read it using `trexio_write_nucleus_coord` or `trexio_read_nucleus_coord` functions, respectively.
Note: the `[variable]` names have to be unique only within the corresponding parent `[group]`. Note: the `[variable]` names have to be unique only within the corresponding parent `[group]`.
There is no naming conflict when, for example, `num` variable exists both in the `nucleus` group (i.e. the number of nuclei) and in the `mo` group (i.e. the number of molecular orbitals). There is no naming conflict when, for example, `num` variable exists both in the `nucleus` group (i.e. the number of nuclei) and in the `mo` group (i.e. the number of molecular orbitals).
These quantities can be accessed using the corresponding `trexio_[has|read|write]_nucleus_num` and `trexio_[has|read|write]_mo_num`, respectively. These quantities can be accessed using the corresponding `trexio_[has|read|write]_nucleus_num` and `trexio_[has|read|write]_mo_num`, respectively.
## Python API ## Python API
For more details regarding the installation and usage of the TREXIO Python API, For more details regarding the installation and usage of the TREXIO Python API,
see [this page](python/README.md). see [this page](python/README.md).
## Tutorial ## Tutorial
TREXIO tutorials in Jupyter notebook format can be found in the TREXIO tutorials in Jupyter notebook format can be found in the
[corresponding GitHub repository](https://github.com/TREX-CoE/trexio-tutorials) [corresponding GitHub repository](https://github.com/TREX-CoE/trexio-tutorials)
or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD). or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD).
For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge: For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb)
@ -110,8 +110,8 @@ For example, the tutorial covering TREXIO basics using benzene molecule as an ex
### Miscellaneous ### Miscellaneous
Note: The code should be compliant with the C99 Note: The code should be compliant with the C99
[CERT C coding standard](https://resources.sei.cmu.edu/downloads/secure-coding/assets/sei-cert-c-coding-standard-2016-v01.pdf). [CERT C coding standard](https://resources.sei.cmu.edu/downloads/secure-coding/assets/sei-cert-c-coding-standard-2016-v01.pdf).
This can be checked with the `cppcheck` tool. This can be checked with the `cppcheck` tool.